Organ failure is a direct cause of a large number of human diseases. Thus, it is impossible to overestimate the potential impact of in vitro organ design and engineering on many fields of medicine. The goal of the SysCODE Consortium is to design engineering approaches to allow the in vitro development of the tooth germ, pancreatic islet and heart valve. The Consortium will seek strategies for organ engineering that will be instructed by the "molecular blueprint" of organogenesis as it occurs in nature, rather than by a blind empirical search. Organ formation in vivo is tightly controlled by complex signaling and regulatory networks and a multitude of micromechanical forces. We hypothesize that detailed characterization of individual components of this network is the most direct way to propel development of a successful organ engineering technology. Most of functional molecular components of this network are ultimately represented by proteins, which play key roles in transmitting signals, regulating gene expression and comprising essential components of the extracellular matrix (ECM). However, the identities of many of these proteins remain unknown, and quantitative information on protein expression is essentially absent. Our existing knowledge of proteins involved in organogenesis comes mainly from genetic methods, especially single gene disruption experiments in mice, rather than from systematic proteomic approaches. Rapid progress in the development of proteomic instrumentation, technology and computational methodology now enables us to begin to identify, quantify and annotate the proteins involved in organogenesis. In conjunction with the mission of the SysCODE Consortium, this proposed project will inform the bioengineering approaches required for the in vitro formation of the tooth germ, pancreatic islet and heart valve. We propose to systematically begin the analysis of the proteomes of these three developing organs by mass spectrometry, and to investigate the dynamic evolution of these proteomes through the key stages of organ development. In Specific Aim 1 we will perform mass spectrometric analyses of proteomes of tooth, pancreatic islet, and heart valve at three sequential stages of development, and in the fully formed organs. We will quantify levels of proteins involved in organogenesis and will monitor their phosphorylation status. In Specific Aim 2, we will build a bioinformatics pipeline to assist protein identification using existing and specifically developed computational approaches. In Specific Aim 3, we will annotate the identified proteins using a variety of bioinformatics techniques. Comparative analysis of proteomes at different stages of organ formation should help reveal proteins with specific functions. We will also compare data on protein expression, mRNA expression and phosphorylation.